Natural conditions and their changes in the late Boreal – early Atlantic period (from ∼8200 to 7700 cal. yr BP) of the Holocene in the Tobol-Ishim interfluve are analyzed based on palynological and zoological materials obtained from archaeological and natural sections and bottom sediments, as well as on the analysis of the hypsographic position of settlements situated on the shores of Lake Mergen (Ishim District of Tyumen Region) where plane-bottomed and round-bottomed Early Neolithic dishes were found. According to author’s reconstruction, the climatic indicators and hydrological regime of Lake Mergen during that part of the Holocene were unstable. The altitude of ancient settlements, the proportion of steppe and forest flora and fauna changed. There were fluctuations in average annual temperatures and the amount of precipitations. The same territory was inhabited by both “local” species and mammals and birds whose habitats fell outside of the region. An Irish Elk (Megaloceros giganteus) of the Pleistocene era was found in the area under consideration. In the late Boreal period, when the water level in the lake was high, people built settlements on floodplain terraces. When the flooding diminished and the seasonal floods ceased, people began to settle on floodplains near the water. Two episodes of aridization can be singled out based on geochemical indicators of bottom sediments of Lake Kyrtyma. One episode was long and had a peak about 6200 cal. yr BP (optimum), another one occurred in the middle of the Sub-Boreal period and was shorter. The informational capacity of geochemical data, as well as that of spore/pollen indicators, is low (at least 100 years) and doesn't reflect short-term paleoclimatic events. The whole spectrum of data should be applied in order to reflect such events. In particular, hypsometric characteristics of ancient settlements are of great importance, because people react to changes in the hydrological regime faster than the flora and fauna do.